The preparation of coffee beans for consumption is a tightly choreographed process. Coffee cherries are harvested upon ripening and then both mechanical and biological processes are employed to recover a coffee bean from each cherry. The production process begins by the mechanical removal of both the outer covering (exocarp) and the pulp (outer mesocarp) in a process referred to as depulping.
A poorly understood fermentation step that has long been speculated to result in hydrolysis of the inner pectin coating is important for the production of suitable coffee beans. Briefly, this step involves soaking coffee beans in a vat of untreated water for approximately 15 to 20 hours. The completion of the fermentation step is then signaled by coffee beans undergoing textural changes to their pectin coating, which is thought to represent the hydrolysis of this layer. Frequent over fermentation results in spoilage and loss of product. Upon the completion of fermentation, the coffee beans are then washed, dried and are ready for roasting to produce the final product.
The fermentation process has been speculated to target the pectin coating of coffee beans. Pectin itself consists of linear polymers of alpha 1-4 linked D-galacturonic acid1. The carboxyl groups are frequently methylated to yield the corresponding ester. The degree of esterification (DE) refers to the ratio of esterified galactouronic groups to the total number of groups, and is used to classify pectin as either high methoxyl pectin (HM) or low methoxyl pectin (LM) at 50% DE′. The functional significance of the DE is its relationship to pectin solubility, gel forming abilities and availability for hydrolysis. Pectins with a lower degree of esterification can enter solution at a lower temperature and require a lower pH for precipitation due to their relative greater hydrophobicity of ester groups when compared with carboxy groups1.
The hydrolysis of pectin is mediated by four classes of enzymes: pectin methyl esterase (PME), polygalactouronases (PG), pectin lyase (PL) and rhamnogalacturonases (RHG)2. The activity of polygalacturonases may be further classified as having either endo- or exo-polygalacturonase activity. Endo-polygalacturonases catalyze the hydrolysis of 1,4-alpha-D-galacturosiduronic linkages between two non-methylated galacturonic acid residues while exo-polygalacturonases remove terminal residues. While, pectin methyl esterases (PME) function to reduce the esterification of pectin and as a consequence create a substrate that is then available for hydrolysis by polygalacturonases2.
The inner pectin coating has been hypothesized to be degraded by both bacterial and endogenous coffee bean enzymes3,4. The development of an acidic environment (pH 5.3-3.5) during the course of fermentation was thought to reflect the growth of presumed pectinolytic bacteria5. Changes in the texture and feel of the pectin coating after fermentation have been presumed to represent the hydrolysis of the pectin coating and signals to coffee producers the point at which fermentation should be terminated6. An incomplete removal of the inner mesocarp has been postulated to act as substrate for subsequent bacterial fermentation and spoilage of the bean7.
Frequent under- or over-fermentation will result in taste defects in the end product and may require disposal of the product8. Yeast overgrowth from a prolonged fermentation, due to their greater tolerance of an acidic environment is thought to be responsible for the taste defects that arise from over-fermentation. Specifically, ethanol production in addition to other organic acids from yeast is thought to be the principal mediator of the bitter taste associated with over-fermentation9.
More recent studies have suggested that the role of bacterial enzymes in fermentation may be dramatically limited in terms of their significance6. An examination of the fermentation microflora revealed that the proportion of pectinolytic bacteria remained relatively stable during fermentation5. Instead, non-pectinolytic lactic acid bacteria and yeast comprised the majority of cell growth, again presumably due to their greater tolerance of acidic conditions5. Pectinolytic bacteria that were recovered from the fermentation process included only those with limited pectinolytic activity, Erwinia herbicola and Klebsiella pneumoniae5. An innoculum enriched with these organisms failed to accelerate or alter fermentation in any meaningful manner to further refute earlier theories of their significance in coffee bean fermentation10. Yeast capable of pectinolysis have yet to be recovered from a fermentation reaction11.
The pectin coating that covers coffee beans exists in a highly esterified form12. As a consequence of this degree of esterification, the activity of pectin methyl esterases are essential to deesterify the pectin which then allows for subsequent substrate availability and hydrolysis by polygalacturonases. It has been observed that without deesterification the pectin would remain essentially unhydrolyzable by bacterial polygalacturonases2. Bacteria recovered from coffee fermentation reactions have to date been repeatedly shown to lack the activity to depolymerize esterified pectins10. The in vitro pectylase activity that has been recovered from bacteria present in coffee fermentation reactions was relatively inactive at the low pH environment at which the fermentation reaction occurs. Instead in vitro assays showed that the maximum catalytic activity for these enzymes was within the alkaline pH range10. Bacteria with polygalacturonase activity compatible with the acidic conditions of fermentation were present in relatively low levels although as previously mentioned they were unable to hydrolyze highly methylated pectin5. Hence, the current view is that bacterially expressed pectinases have no significant role in coffee fermentation. This notion is further reinforced by examination of coffee beans post fermentation to reveal that only modest depolymerization and limited hydrolysis of the pectin covering occurs6.
In summary, the limited growth of pectinolytic bacteria during the fermentation process, an absence of PME activity and finally the basic pH requirements of the limited pectinolytic activity that was present are all strongly suggestive of the current view that bacteria play a very limited or no role in directly mediating pectin hydrolysis. Avallone et al. have proposed an alternative mechanism that bacterially produced organic acids (lactic and acetic acid) decrease the environmental pH to induce conformational changes in pectin that results in it subsequent depolymerization6. This current view of coffee fermentation is in sharp contrast to previous theories that bacterial enzymes drive fermentation by catalyzing pectin hydrolysis.